6-8361158-A-G

Variant names:

• chr6-8361158-A-G
• rs6920684
• ENST00000644718.1:n.560+53598A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000644718.1(ENSG00000285216):​n.560+53598A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,936 control chromosomes in the GnomAD database, including 29,020 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (29020 hom., cov: 31)
• Consequence: ENSG00000285216 ENST00000644718.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539

Genes affected

ENSG00000285216 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285216	ENST00000644718.1	n.560+53598A>G		intron_variant	Intron 5 of 8
ENSG00000234763	ENST00000651914.1	n.311+1562T>C		intron_variant	Intron 4 of 4
ENSG00000234763	ENST00000655767.1	n.341+1562T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92367 AN: 151816 Hom.: 29007 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.605

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.608 AC: 92410 AN: 151936 Hom.: 29020 Cov.: 31 AF XY: 0.619 AC XY: 45975 AN XY: 74230

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.610

Alfa AF: 0.623 Hom.: 14883

Bravo AF: 0.599

Asia WGS AF: 0.830 AC: 2883 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6920684; hg19: chr6-8361391;